The expression of virulence factors in the bacterium Bordetella pertussis is regulated in an environmentally responsive fashion under the control of the two-component system encoded by the bvgAS locus. In recent years we have focused research efforts on understanding the mechanisms of gene regulation in this important human pathogen - specifically focussing on the genes encoding pertussis toxin (ptx) and filamentous hemagglutinin (fha). Within the past year we have elucidated some details regarding the interaction of the BvgA response regulator protein with RNA polymerase at the promoters for these virulence genes. We have studied DNA-binding of BvgA and mutants which either do not express the ptx genes, or which express them at elevated levels and have documented their activities in in vitro transcription assays. In addition we have examined interactions of BvgA with RNA polymerase, both genetically, by isolating mutations in the gene encoding the alpha subunit of RNA polymerase which affect virulence gene regulation, and biochemically, by determining which amino acids on the alpha subunit contact BvgA at the ptx and fha promoters. Interestingly, these contacts appear to differ at the two promoters. Other studies in the laboratory have addressed the genomic structure of natural isolates of B. pertussis from a recent outbreak. We found that gene order in the chromosomes of these strains was variable.